Magnesium in PDB 3mby: Ternary Complex of Dna Polymerase Beta with Template Base A and 8OXODGTP in the Active Site with A Dideoxy Terminated Primer

Enzymatic activity of Ternary Complex of Dna Polymerase Beta with Template Base A and 8OXODGTP in the Active Site with A Dideoxy Terminated Primer

All present enzymatic activity of Ternary Complex of Dna Polymerase Beta with Template Base A and 8OXODGTP in the Active Site with A Dideoxy Terminated Primer:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex of Dna Polymerase Beta with Template Base A and 8OXODGTP in the Active Site with A Dideoxy Terminated Primer, PDB code: 3mby was solved by V.K.Batra, W.A.Beard, E.W.Hou, L.C.Pedersen, R.Prasad, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	19.84 / 2.00
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	50.830, 80.030, 55.420, 90.00, 107.70, 90.00
*R / R_free (%)*	19 / 24.6

Other elements in 3mby:

The structure of Ternary Complex of Dna Polymerase Beta with Template Base A and 8OXODGTP in the Active Site with A Dideoxy Terminated Primer also contains other interesting chemical elements:

Chlorine	(Cl)	3 atoms
Sodium	(Na)	3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ternary Complex of Dna Polymerase Beta with Template Base A and 8OXODGTP in the Active Site with A Dideoxy Terminated Primer (pdb code 3mby). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Ternary Complex of Dna Polymerase Beta with Template Base A and 8OXODGTP in the Active Site with A Dideoxy Terminated Primer, PDB code: 3mby:

Magnesium binding site 1 out of 1 in 3mby

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Magnesium Binding Sites List in 3mby

Magnesium binding site 1 out of 1 in the Ternary Complex of Dna Polymerase Beta with Template Base A and 8OXODGTP in the Active Site with A Dideoxy Terminated Primer

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ternary Complex of Dna Polymerase Beta with Template Base A and 8OXODGTP in the Active Site with A Dideoxy Terminated Primer within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg339 b:17.6 occ:1.00	O1A	A:8DG338	1.9	24.8	1.0
	OD1	A:ASP190	1.9	19.1	1.0
	OD2	A:ASP192	2.0	16.0	1.0
	O2B	A:8DG338	2.0	16.6	1.0
	O3G	A:8DG338	2.0	18.6	1.0
	O	A:HOH379	2.4	18.7	1.0
	CG	A:ASP190	2.9	21.7	1.0
	CG	A:ASP192	3.0	17.3	1.0
	PB	A:8DG338	3.1	19.9	1.0
	PA	A:8DG338	3.2	23.2	1.0
	NA	A:NA340	3.3	24.0	1.0
	PG	A:8DG338	3.3	23.1	1.0
	OD2	A:ASP190	3.3	24.9	1.0
	OD1	A:ASP192	3.4	21.1	1.0
	O3A	A:8DG338	3.5	21.1	1.0
	O3B	A:8DG338	3.5	20.7	1.0
	O	A:ASP190	3.9	17.8	1.0
	O2G	A:8DG338	4.0	19.7	1.0
	C	A:ASP190	4.2	17.6	1.0
	O5'	A:8DG338	4.2	20.9	1.0
	O2A	A:8DG338	4.2	22.6	1.0
	CB	A:ASP190	4.2	19.0	1.0
	C5'	A:8DG338	4.3	21.8	1.0
	O1G	A:8DG338	4.3	23.8	1.0
	N	A:ASP190	4.3	16.1	1.0
	CB	A:ASP192	4.4	18.2	1.0
	O	A:HOH390	4.4	18.8	1.0
	CA	A:ASP190	4.5	18.2	1.0
	O1B	A:8DG338	4.5	20.1	1.0
	CA	A:GLY179	4.6	16.4	1.0
	OG	A:SER180	4.6	20.7	1.0
	N	A:SER180	4.6	18.2	1.0
	N	A:MET191	4.7	17.7	1.0
	N	A:ASP192	4.8	18.0	1.0
	O	A:HOH553	4.9	29.1	1.0
	O	P:HOH306	4.9	37.8	1.0
	C	A:MET191	4.9	17.9	1.0

Reference:

V.K.Batra, W.A.Beard, E.W.Hou, L.C.Pedersen, R.Prasad, S.H.Wilson. Mutagenic Conformation of 8-Oxo-7,8-Dihydro-2'-Dgtp in the Confines of A Dna Polymerase Active Site. Nat.Struct.Mol.Biol. V. 17 889 2010.
ISSN: ISSN 1545-9993
PubMed: 20526335
DOI: 10.1038/NSMB.1852

Page generated: Mon Aug 11 00:31:13 2025

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